mecfs_bio.build_system.task.genome_reference_harmonization

Modules:

• allele_classes –

  Per-row allele classes relative to the genome reference.

• ambiguous_indels –

  Stringent resolution of ambiguous indels (both alleles on the genome) in untrusted tables.

• fasta –

  Memory-mapped access to an uncompressed, faidx-indexed genome FASTA.

• flip –

  How each summary-statistic column changes when a variant's effect allele is swapped.

• genome_reference_harmonization_task –

  Genome-reference harmonization of GWAS summary statistics.

• gnomad –
• indexed_fasta_task –

  Decompress a gzipped genome FASTA and index it with faidx.

• options –

  Options for genome-reference harmonization, validated at construction.

• outcomes –

  Named outcomes of genome-reference harmonization: allele actions, palindrome decisions

• palindromes –

  Strand resolution of palindromic SNVs in untrusted tables: gwaslab's rule plus a distance check.

• pan_ukbb –
• panel_batch_checks –

  Invariants shared by the allele-frequency panel extraction Tasks, applied batch by batch.

• reference_panel_task –

  Convert a reference panel VCF into a sites-only allele-frequency parquet.

• resolve_chromosome –

  Resolve one chromosome of summary statistics against the genome reference.

• trust –

  Whether a table's NEA column is trustworthy as the reference allele.